For Shadow Tactics: Blades of the Shogun: Aiko’s Choice players, this guide will explain all 44 achievements arranged by category, let’s check them out.
Stuff you want to know about
Approximate amount of time to 100%: 15 to 20 hours
Minimum number of playthroughs needed: There is chapter select and missions will have to be replayed several times to get badges.
Number of missable achievements: 0
Does difficulty affect achievements?: No
44 Total Achievements
7 Secret Achievements – Hidden achievements that you can unlock accidentally or by following a guide like this
15 Special Achievements – These are like challenges
16 Grind Achievements – These achievements require a bit of grinding
6 Story Achievements – These achievements automatically unlock as you progress the story
(The screenshot below is not for an achievement but for the badge (Nagoya City): Kill 5 enemies at the same time with Mugen’s Sword Wind.)
Secret (Hidden) Achievements
Equip a disguise on Aiko, quicksave then press D and click on the Samurai to talk to him. Quickload and continue your mission.
In the mission Toba Coastline, look for a small empty island in the middle of the map. Bring your characters in the island and it will trigger a conversation.
In the mission Nagoya City, swim on one side of the river to come out on the other side.
You should unlock this on your first playthrough of this mission. Just swim around until the achievement pops. 
In the mission Hana Gakuen, there is a Shrine riddle at the beginning. The correct answer is bird-monkey-frog. Touch the stones in the wrong order and fail 3 times.
In the Epilogue mission, interact with Kuma several times to talk to him until you get the achievement.
Special Achievements
In any mission where you have all 5 characters, use Shadow Mode and execute a walk command on all 5 characters.
In any mission where you have all 5 characters, use Shadow Mode to kill or knock out 5 guards at the same time. If you are having trouble doing this during normal play, just knock out 4 guards, use shadow mode to have Hayato, Yuki, Mugen, and Aiko kill the 4 guards and have Takuma snipe a fifth guard.
In the mission Hana Gakuen, have Mugen pick up the big rock and throw it at a samurai.
You can unlock this during the first mission. Throw the guard into the well after killing/knocking him out. 
Use Kuma to attract the guard where a samurai and straw hat is talking then drop the box on them.
Only use Takuma’s sniper rifle to stun a samurai.
In the mission Hana Gakuen, don’t get a disguise for Aiko. Kill Lady Chiyo using explosives or poison (mission objective). Don’t kill Lady Chiyo using other characters as this will not count.
In the mission Hana Gakuen, use Takuma’s bomb to kill Lady Chio. Stand just behind the gate and throw the bomb near Lady Chio while she speaks with the crowd.
Alternate method from Steam User heidi:
For What’s Done is Done, you can also shoot Lady Chiyo with any of Hayato, Yuki or Aiko by jumping up to the temple in front of the shrine. Lady Chiyo just passes in range of the flintlock when walking from the theater to the shrine.
(The Temple)
Open all the hidden caves in Hana Gakuen by interacting with the bird statue located all over the map. There are 5 hidden caves. Use Highlight (default key: H) and scan your map to make sure you don’t miss any. The achievement will pop up after completing the mission.
Cave 1 & 2
Cave 3
Cave 4
Cave 5
Grind Achievements
See Shinobi.
See Shinobi.
You will unlock this on your first playthrough. There are many enemies in the main missions.
See Masterful.
See Masterful.
Start doing this as soon as the first mission. You can complete this in just 1 playthrough.
You can easily complete this during the mission Hana Gakuen. Use the environment traps as often as possible. You can get around 20+ kills on this map alone.
To easily unlock this, find a guard that is far away. Quicksave then kill the guard using Takuma’s rifle. Quickload then do it again. Repeat until you get the achievement.
You will unlock this during normal playthrough. Use sword wind on groups of enemies.
You can unlock this as soon as you get your first disguise. Equip the disguise then crouch to unequip it. Repeat until you get the achievement.
To kill a samurai, stun him first by shooting (gun icon skill) him using another character other than Yuki. Make sure you are far enough (not within the blue circle) so the samurai can’t shoot you back. Use Yuki (approach from the samurai’s blind spot) to kill the samurai. Do this 3 times to get the achievement.
You can distract the same enemies as many times as you want using Hayato’s stone.
Slash enemies after dropping on them from a roof, rope or any high places.
Use sword wind on groups of enemies (except if there is a samurai with them).
Interact with the trap switch when a guard is in front of the trap. You can lure them using Yuki’s whistle, Mugen’s sake or Kuma. 
There are 3 missions where you can get badges. Each mission has 9 badges so there are 27 total badges and you only need to get 17. You cannot complete all 9 badges in 1 playthrough. You cannot earn a badge on the easiest difficulty. Play on normal difficulty on your first playthrough and don’t worry about the badges, you cannot see them yet. You may need to play some missions multiple times to get the badges. You can also play on Hardcore mode, it’s not that hard once you know what to do. 
Story Achievements
This is a story related achievement and cannot be missed.
This is a story related achievement and cannot be missed.
This is a story related achievement and cannot be missed.
This is a story related achievement and cannot be missed.
This is a story related achievement and cannot be missed.
This is a story related achievement and cannot be missed.